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    Optc opticin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304802, updated on 10-Oct-2024

    Summary

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    Official Symbol
    Optcprovided by RGD
    Official Full Name
    opticinprovided by RGD
    Primary source
    RGD:1304916
    See related
    EnsemblRapid:ENSRNOG00000003059 AllianceGenome:RGD:1304916
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in collagen fibril organization. Predicted to act upstream of or within negative regulation of angiogenesis. Predicted to be active in extracellular matrix. Orthologous to human OPTC (opticin). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 8.0), Lung (RPKM 6.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Optc in Genome Data Viewer
    Location:
    13q13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (47906145..47920334, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (45353954..45368254, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (50735509..50748908, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene ATPase plasma membrane Ca2+ transporting 4 Neighboring gene uncharacterized LOC134481499 Neighboring gene uncharacterized LOC134481498 Neighboring gene uncharacterized LOC102557118 Neighboring gene proline and arginine rich end leucine rich repeat protein Neighboring gene uncharacterized LOC134481559 Neighboring gene uncharacterized LOC134481558

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. In vivo effect of opticin deficiency in cartilage in a surgically induced mouse model of osteoarthritis. Farrán A, et al. Sci Rep, 2018 Jan 11. PMID 29323130, Free PMC Article
    2. The vitreous glycoprotein opticin inhibits preretinal neovascularization. Le Goff MM, et al. Invest Ophthalmol Vis Sci, 2012 Jan 25. PMID 22159013, Free PMC Article
    3. Identification of opticin, a member of the small leucine-rich repeat proteoglycan family, in human articular tissues: a novel target for MMP-13 in osteoarthritis. Monfort J, et al. Osteoarthritis Cartilage, 2008 Jul. PMID 18164633
    4. Female-specific hypertension loci on rat chromosome 13. Hoffman MJ, et al. Hypertension, 2013 Sep. PMID 23817491, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    acts_upstream_of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in articular cartilage development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in bone development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of angiogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    opticin

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001395559.1 → NP_001382488.1  opticin precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A096MJH6
      Conserved Domains (3) summary
      PRK15370
      Location:212 → 342
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PRK15387
      Location:156 → 260
      PRK15387; type III secretion system effector E3 ubiquitin transferase SspH2
      sd00033
      Location:169 → 192
      LRR_RI; leucine-rich repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      47906145..47920334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039090712.2 → XP_038946640.1  opticin isoform X1

      UniProtKB/TrEMBL
      A6IC95
      Conserved Domains (3) summary
      PRK15370
      Location:270 → 366
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:226 → 250
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:228 → 285
      LRR_8; Leucine rich repeat

    2. XM_063272294.1 → XP_063128364.1  opticin isoform X2

      UniProtKB/TrEMBL
      A0A096MK02
      Related
      ENSRNOP00000068329.1, ENSRNOT00000076673.4

    3. XM_039090714.2 → XP_038946642.1  opticin isoform X3

      Conserved Domains (2) summary
      PRK15370
      Location:34 → 187
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:49 → 71
      LRR_RI; leucine-rich repeat [structural motif]

    4. XM_063272297.1 → XP_063128367.1  opticin isoform X5

    5. XM_063272295.1 → XP_063128365.1  opticin isoform X4

    RNA

    1. XR_010056916.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107176.1: Suppressed sequence

      Description
      NM_001107176.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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